Detailed Schedule, q-bio16, Fort Collins

Below we will place the schedule of the 2016 q-bio Summer School as it begins to evolve. Please keep in mind that this is subject to change up to the last minute.

Description of events:

• General Seminars, Keynote Presentations, and Invited Talks - These are traditional seminar style presentations. These are open and available to the public. Many of these will be video-recorded and later posted online. The majority of the seminar talks will take place in Scott 229.

• Chalk Talks - This is a more in-depth discussion or pedagogical lecture on a topic. These are open to registered participants or with consent from the organizers. A select few of these will be video-recorded and later posted online.

• Breakout Sessions - These are more tutorials or software demonstrations. These are open to registered participants or with consent from the organizers.

• Student Talks - These are 15 minute student presentations. These are open to registered participants and to the public with consent of each presenter.

• Panel Discussions - These are 1 hour discussions of topics of particular importance to young researchers in q-bio (e.g, choosing career paths, forming collaborations, writing proposals, etc).

Week 1, July 10-15, 2016

Sunday, July 10, 2016

• 17:00-20:00 Welcome reception, Scott Building Atrium

Monday, July 11, 2016

• 08:10-08:30 Introduction to the 2016 q-bio Summer School, Scott Building, Room 229
  • 08:10-08:20 Introductions, Brian Munsky
  • 08:20-08:30 Welcome, David McLean, Dean of College of Engineering, CSU
• 08:30-09:20 Introduction Seminar 1, Brian Munsky and Doug Shepherd, Introduction to Stochastic Gene Regulation, Scott Building, Room 229
• 09:30-10:20 Introduction Seminar 2, Marek Kimmel and Rosemary Braun, Introduction to Cancer Dynamics, Scott Building, Room 229
• 10:30-11:20 Introduction Seminar 3, Patrick Shipman, Steve Haase, and Francis Motta, Introduction to Complex Biological Dynamics, Scott Building, Room 229
• 11:30-13:00 Lunch
• 13:15-14:15 Practical Preliminaries
  • Scientific Computing in Matlab, Patrick Shipman, Scott Building, Room 229
  • Introduction to Bayesian Analysis, Brian Munsky, Scott Building, Room 231
• 14:30-15:30 Practical Preliminaries
  • Introduction to Information Theory, Rosemary Braun, Scott Building, Room 229
  • Introduction to Monte Carlo Methods, Doug Shepherd, Scott Building, Room 231
• 15:30-17:30 Breakout Sessions -- Group Project Descriptions
  • Single-cell Gene Regulation (SGR), Scott Building, Room 229
  • Cancer Dynamics (CD), Scott Building, Room 209
  • Complex Biological Dynamics (CBD), Scott Building, Room 231
• 17:30-20:00 Opening Poster Session, Scott Building Atrium (drinks and hors d'oeuvres will be served).
  • 18:00-18:10 Welcome, Alan Rudolph, Vice President for Research, CSU.

Tuesday, July 12, 2016

• 08:30-09:30 General Seminar 1, David Axelrod, Rutgers University, Breast Cancer: Deterministic Modeling of Tumor Progression Based Upon Clinical Histopathology Data, Scott Building, Room 229
• 09:45-10:45 Coffee Break and Panel Discussion 1, Choosing the right research project, Scott Building, Room 229
• 11:00-12:15 Student Talks 1-4, Scott Building, Room 229
  • 11:00-11:15, Aaron Prescott, University of Tennessee, Redesigning Signaling Network Responses Using In Silico Evolution
  • 11:15-11:30, Krishna Kanhaiya, Åbo Akademia, Sweden
  • 11:30-11:45, Kenneth Lyon, Colorado State University
  • 11:45-12:00, Taylor Firman, University of Denver
• 12:15-14:00 Lunch
• 14:00-15:00 Chalk Talk, Brian Munsky and Doug Shepherd, Stochastic Simulation Algorithm and Kinetic Monte Carlo: Theory and Derivations, Scott Building, Room 229
• 15:15-17:30 Breakout Sessions
  • (SGR/CD/CBD) Computer Lab -- Stochastic Simulation Algorithm, Multiple Small Group Programming Sessions, Locations TBA.
• 17:30-19:15 Dinner Break (Note: Dining Commons Stop Serving Dinner at 18:30pm)
• 19:30-21:00 Project Work

Wednesday, July 13, 2016

• 08:30-09:30 General Seminar 2, Patrick Shipman, Introduction to Bifurcation Theory, Scott Building, Room 229
• 08:30-09:30 Special Seminar (CD), David Axelrod, Rutgers University, Colon Cancer: Stochastic Modeling of Stem Cell Dynamics to Improve Treatment and Prevention, Scott Building, Room 231
• 09:45-10:45 Coffee Break and Panel Discussion 2, Finding a good postdoc position, Scott Building, Room 229, Chair: Rosemary Braun
  • Resources for students seeking postdocs
• 11:00-12:15 Student Talks 5-8, Scott Building, Room 229
  • 11:00-11:15, Mona Katharina Ton, Imperial College London
  • 11:15-11:30, Santosh Manicka, Indiana University Bloomington
  • 11:30-11:45, Mahan Ghafari, Emory University
  • 11:45-12:00, Martijn Wehrens, FOM Institute AMOLF, Noise, dynamic regulation and growth in bacteria
• 12:15-14:00 Lunch
• 14:00-15:00 General Seminar 3, Steve Haase, Duke University, Structure and Function of Biological Clocks, Scott Building, Room 229
• 15:15-17:30 Breakout Sessions
  • (SGR) Computer Lab -- Brian Munsky, Basic Finite State Projection Algorithm Approaches, Scott Building, Room 229
  • (CBD) Biology and Dynamical Models of GRNs, Scott Building, Room 235
  • (CD) Cancer Biomedical Background - Part 1, David Axelrod, Scott Building, Room 231
• 17:30-19:15 Dinner Break (Note: Dining Commons Stop Serving Dinner at 18:30pm)
• 19:30-21:00 Special Evening Workshop -- Brian Drawert, StochSS Tutorial, Scott Building, Room 229

Thursday, July 14, 2016

• 08:30-09:30 General Seminar 4, Rosemary Braun, "Hearing the Shape" of Complex Disease, Scott Building, Room 229, Note Change in time.
• 09:45-10:45 Coffee Break and Panel Discussion 3, Balancing work and family in a research career, Scott Building, Room 229
• 11:00-12:15 Student Talks 9-12, Scott Building, Room 229
  • 11:00-11:15, Qiuyan Shao, Texas A&M University, Increased noisiness in gene expression caused by DNA replication reinforces the cell-fate decision by bacteriophage lambda
  • 11:15-11:30, Kun Xiong, University of Arizona
  • 11:30-11:45, Zachary Fox, Colorado State University
  • 11:45-12:00, Max Wilson, Princeton University
• 12:15-14:00 Lunch
• 14:00-15:00 General Seminar 5, Sabrina Spencer, Single-cell dynamics of the proliferation-quiescence decision, Scott Building, Room 229, Note change in time.
• 15:15-17:30 Breakout Sessions
  • (SGR) Chalk Talk and Computer Lab -- Brian Munsky, Advanced Finite State Projection Algorithm Analysis, Scott Building, Room 229
  • (CBD) Seminar and Computer Lab -- Francis Motta and Tina Kelliher, Periodicity Detection Algorithms and Implementation, Scott Building, Room 235
  • (CD) Seminar -- Cancer Biomedical Background - Part 2, David Axelrod, Scott Building, Room 231
• 17:30-19:15 Dinner Break (Note: Dining Commons Stop Serving Dinner at 18:30pm)
• 19:30-21:00 Project Work

Friday, July 15, 2016

• 08:30-09:30 General Seminar 6, Roy Wollman, Scott Building, Room 229
• 09:45-10:45 Coffee Break and Panel Discussion 4, Applying for grants and fellowships, Scott Building, Room 229, Chair: Shing Ho
• 11:00-12:15 Student Talks 13-16, Scott Building, Room 229
  • 11:00-11:15, Chengzhe Tian, University of Copenhagen, Digital signaling decouples activation probability and population heterogeneity
  • 11:15-11:30, Mingwei Min
  • 11:30-11:45, Kerrigan Blake, University of California, Irvine, Not Your Average Tissue: Single Cell RNA-Seq in Human Epithelia
  • 11:45-12:00, Sina Jazani, Indiana University - Purdue University at Indianapolis
• 12:15-14:00 Lunch
• 14:00-15:00 General Seminar 7, Marek Kimmel, TBA, Scott Building, Room 229
• 15:15-17:30 Breakout Sessions
  • (SGR) Chalk Talk -- Roy Wollman, Information Theory and Analyses, Scott Building, Room 229
  • (CBD) Talk and Computer Lab -- Steve Haase, Francis Motta, and Tina Kelliher, Experimental Edge Finding, LEM theory and implementation, Scott Building, Room 235
  • (CD) Seminar -- Rosemary Braun, Network Analysis of *Omic Data (Part 1), Scott Building, Room 231
• 17:30-19:15 Dinner Break (Note: Dining Commons Stop Serving Dinner at 18:30pm)

Weekend, July 16-17, 2016

• July 16, 2016, Explore Northern Colorado or take the New Belgium Brewery tour.
• July 17, 2016, Explore Northern Colorado

Week 2, July 18-22, 2016

Monday, July 18, 2016

• 08:30-09:30 General Seminar 8, Michael Savageau, A Rigorous Definition of Phenotype Enabling A Phenotype-Centric Modeling Strategy, Scott Building, Room 229
• 09:45-10:45 Coffee Break and Panel Discussion 5, Building multidisciplinary collaborations, Scott Building, Room 229
• 11:00-12:15 Project work
• 12:15-14:00 Lunch
• 14:00-15:00 General Seminar 9 Tim Stasevich, Imaging Nascent Translation from a Single mRNA, Scott Building, Room 229. Please install Design Space Toolbox V2 Located here
• 15:15-17:30 Breakout Sessions
  • (SGR) Tutorial -- Michael Savageau, Uncovering Design Principles, Scott Building, Room 229
  • (CBD) Talk -- Steve Haase, Francis Motta, Network Motiffs, Scott Building, Room 203
  • (CD) Lecture/Lab -- ​Andrzej Polanski and Marek Kimmel, Evolutionary Models for Cancer Genomics (part 1), Scott Building, Room 231
• 17:30-19:15 Dinner Break (Note: Dining Commons Stop Serving Dinner at 18:30pm)
• 19:30-21:00 Project Work

Tuesday, July 19, 2016

• 08:30-09:30 General Seminar 10, James Ferrell, Scott Building, Room 229
• 09:45-10:45 Coffee Break and Panel Discussion 6, Navigating the tenure process in academia, Scott Building, Room 229
• 11:00-12:15 Student Talks 17-20, Scott Building, Room 229
  • 11:00-11:15, Rebecca Brouwers, University of Edinburgh
  • 11:15-11:30, Xueping Zhao, University of South Carolina, Hydrodynamic Theories for Pattern Formation in Clusters of Stem Cells and Differentiated Cells
  • 11:30-11:45, Danny Dhokarh, Mayo Clinic
  • 11:45-12:00, Monika Kurpas, Silesian University of Technology
• 12:15-14:00 Lunch
• 14:00-15:00 General Seminar 11, Steve Presse, Scott Building, Room 229
• 15:15-17:30 Breakout Sessions
  • (SGR) Derivation Session -- Steve Presse, Maximum Entropy, Scott Building, Room 229
  • (CBD) Journal Club -- Steve Haase, Francis Motta, Rahi, et al. paper, Scott Building, Room 235
  • (CD) 15:15-17:30 Lecture/Lab -- ​Andrzej Polanski and Marek Kimmel, Evolutionary Models for Cancer Genomics (part 2), Scott Building, Room Room 231, Note Change in Room
• 17:30-19:15 Dinner Break (Note: Dining Commons Stop Serving Dinner at 18:30pm)
• 19:30-21:00 Project Work

Wednesday, July 20, 2016

• 08:30-09:30 General Seminar 12, Tomas Gedeon, A new approach to dynamical models in biology using switching networks, Scott Building, Room 229
• 09:45-10:45 Coffee Break and Panel Discussion 7, Resolving Conflicts in Mentor/Mentee Relationships, Scott Building, Room 229
• 11:00-12:15 Student Talks 21-24, Scott Building, Room 229
  • 11:00-11:15, Niccolò Totis, University of Turin, Italy
  • 11:15-11:30, TBD
  • 11:30-11:45, Michael Wolfe, University of Michigan
  • 11:45-12:00, Elaheh Alizadeh, Colorado State University, Systematic changes in invasive cancer cell shape
• 12:15-14:00 Lunch
• 14:00-15:00 General Seminar 13, Joel Kralj, Optical Voltage Imaging in Cells and Organisms, Scott Building, Room 229
• 15:15-17:30 Breakout Sessions
  • (SGR) Computer Lab -- Doug Shepherd, Image Processing Tools and Methods, Scott Building, Room 229
  • (CBD) Talk and Computer Lab -- Steve Haase, Francis Motta, Tomas Gedoen DSGRN Theory and Implementation, Scott Building, Room 235
  • (CD) Lecture/Lab -- ​Andrzej Polanski and Marek Kimmel, Evolutionary Models for Cancer Genomics (part 3), Scott Building, Room 231
• 17:30-19:15 Dinner Break (Note: Dining Commons Stop Serving Dinner at 18:30pm)
• 19:30-21:00 Project Work

Thursday, July 21, 2016

• 08:30-09:30 General Seminar 14, Seth Corey, Dynamics of Leukemia, Scott Building, Room 229
• 09:45-10:45 Coffee Break and Panel Discussion 8, Intellectual Property (IP) and Entrepreneurship, Scott Building, Room 229, Chair: Stu Tobet
• 11:00-12:15 Project work
• 12:15-14:00 Lunch
• 14:00-15:00 General Seminar 15, Cecilia Diniz-Behn, Multiscale Modeling of Biological Rhythms, Scott Building, Room 229
• 15:15-17:30 Breakout Sessions
  • (SGR) Computer Lab -- Parameter Fitting and Inference Approaches, Scott Building, Room 229
  • (CBD) Talk and Computer Lab -- Steve Haase, Francis Motta, Tomas Gedoen, Global optimization of parameters, Scott Building, Room 231
• 17:30-19:15 Dinner Break (Note: Dining Commons Stop Serving Dinner at 18:30pm)
• 19:30-21:00 Project Work

Friday, July 22, 2016

• 08:30-09:30 General Seminar 16, Alexandra Jilkine, The role of cell location and spatial gradients in the evolutionary dynamics of the intestinal crypt, Scott Building, Room 229
• 09:45-10:45 Coffee Break and Panel Discussion, Topic to be chosen by students, Scott Building, Room 229
• 11:00-12:15 Project Work
• 12:15-14:00 Lunch
• 14:00-17:00 Project Presentations, Scott Building, Room 229
• 17:00-17:30 Closing Remarks and Farewell, Scott Building, Room 229
• 17:30-19:15 Dinner Break (Note: Dining Commons Stop Serving Dinner at 18:30pm)

Weekend, July 23-24, 2016

• July 23, 2016 -- Work on Course Project Write-up
• July 24, 2016 -- Travel to Nashville, TN (on own).

Week 3, July 25-30, 2016

• July 25-26, 2016 q-bio Student Symposium, Vanderbilt University, Nashville, TN, USA.
• July 27-30, 2016 10th Annual q-bio Conference, Vanderbilt University, Nashville, TN, USA.